SAXSdb — 4fxy

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neurolysin, mitochondrial

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;1-{(2S)-1-[(3R)-3-(2-chlorophenyl)-2-(2-fluorophenyl)pyrazolidin-1-yl]-1-oxopropan-2-yl}-3-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]urea ; × 1 ZINC ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;1-{(2S)-1-[(3R)-3-(2-chlorophenyl)-2-(2-fluorophenyl)pyrazolidin-1-yl]-1-oxopropan-2-yl}-3-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]urea ; × 1 ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEUL_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain P； PDBConstruct 13–693； UniProt 24–704 Author chain Q； PDBConstruct 13–693； UniProt 24–704

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4fxy
Deposition date deposition_date	2012-07-03
Structure title title	Crystal structure of rat neurolysin with bound pyrazolidin inhibitor
Keywords keywords	hydrolase, endopeptidase, zinc metallopeptidase, neuropeptidase, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4fxy__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4fxy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4fxy__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	27.36 Å
Rg (electron density)	26.31 Å
Total Rg	27.23 Å
Atom count	5373
Residues	664
Excluded volume	95689 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4fxy__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4fxy__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Neurolysin, mitochondrial
Molecular weight formula_weight	79377.6 kDa
EC 编号 ec_number	3.4.24.16
Mutation mutation	H160A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q
Atom count atom_count	11003

DRWIRPRDLQMVMTLGKELASPLQAMSSYTAAGRNVLRWDLSPEQIKTRTEQLIAQTKQVYDTVGTIALKEVTYENCLQVLADIEVTYIVERTMLDFPQHVSSDREVRAASTEADKKLSRFDIEMSMREDVFQRIVHLQETCDLEKIKPEARRYLEKSIKMGKRNGLHLSEAIRNEIKSMKKRMSELCIDFNKNLNEDDTSLVFSKAELGALPDDFIDSLEKTDEDKYKVTLKYPHYFPVMKKCCVPETRRKMEMAFHTRCKQENTAILQQLLPLRAQVAKLLGYNTHADFVLELNTAKSTSRVAAFLDDLSQKLKPLGEAEREFILSLKKKECEERGFEYDGKINAWDLHYYMTQTEELKYSVDQESLKEYFPIEVVTEGLLSIYQELLGLSFEQVPDAHVWNKSVSLYTVKDKATGEVLGQFYLDLYPREGKYNHAACFGLQPGCLLPDGSRMMSVAALVVNFSQPVAGRPSLLRHDEVRTYFHEFGHVMHQICAQTDFARFSGTNVETDFVEVPSQMLENWVWDVDSLRKLSKHYKDGHPITDELLEKLVASRLVNTGLLTLRQIVLSKVDQSLHTNATLDAASEYAKYCTEILGVAATPGTNMPATFGHLAGGYDGQYYGYLWSEVFSMDMFHSCFKKEGIMNPEVGMKYRNLILKPGGSLDGMDMLQNFLQREPNQKAFLMSRGLNGS

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;1-{(2S)-1-[(3R)-3-(2-chlorophenyl)-2-(2-fluorophenyl)pyrazolidin-1-yl]-1-oxopropan-2-yl}-3-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]urea ;
Molecular weight formula_weight	525.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	257

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4fxyp_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.5 — Neurolysin-like

Domain ID domain_id	d4fxyq_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.5 — Neurolysin-like

CATH v4.4 (6 domains)

Domain ID domain_id	4fxyP01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	40 — Endopeptidase. Chain P; domain 1

Domain ID domain_id	4fxyP02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily	10 — Neurolysin, domain 3

Domain ID domain_id	4fxyP03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	4fxyQ01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	40 — Endopeptidase. Chain P; domain 1

Domain ID domain_id	4fxyQ02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily	10 — Neurolysin, domain 3

Domain ID domain_id	4fxyQ03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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Unit-cell length a length_a	88.000 Å
Unit-cell length b length_b	131.400 Å
Unit-cell length c length_c	144.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	48.654 Å
R factor r_factor	0.2403
R_work r_work	0.2349
R_free r_free	0.2871

Crystal structure of rat neurolysin with bound pyrazolidin inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Neurolysin, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4fxy__assembly_1__model_1

4fxy__assembly_1__model_1 | I(q)

4fxy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of rat neurolysin with bound pyrazolidin inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Neurolysin, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4fxy__assembly_1__model_1

4fxy__assembly_1__model_1 | I(q)

4fxy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)